invertmeeg - A high-level M/EEG Python library for EEG inverse solutions 🎯

This package contains various approaches to solve the M/EEG inverse problems ↩️. It integrates with the mne-python framework.

Read the Documentation here.

Install the package from pypi:

Installation

pip install invertmeeg

To check if the installation works run:

python -c 'import invert'

To test the package simply run:

pytest tests

Usage

To calculate an inverse solution using minimum norm estimates simply type:

from invert import Solver

# fwd = ...
# evoked = ...

# Create a Solver instance
solver_name = "MNE"
solver = Solver(solver_name)

# Calculate the inverse operator
solver.make_inverse_operator(fwd)

# Apply the inverse operator to your data
stc = solver.apply_inverse_operator(evoked)

# Plot the resulting source estimate
stc.plot()

There are many solvers implemented in the package, and you can find them here.

:mail: Send feedback or feature requests to lukas.hecker.job@gmail.com

License

©️ This package is licensed under the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) License. See the LICENSE file for details.

Citation

📄 If you use this package and publish results, please cite as:

@Misc{invertmeeg2022,
  author =   {{Lukas Hecker}},
  title =    {{invertmeeg}: A high-level M/EEG Python library for EEG inverse solutions.},
  howpublished = {\url{https://github.com/LukeTheHecker/invert}},
  year = {since 2022}
}

List of Algorithms

📚 This is the exhaustive list of all implemented algorithms to solve the M/EEG inverse problem.

:mail: Can't find yours? Send me an email with the implementation in python and I will do my best to add it.

Minimum Norm

Full Solver Name	Abbreviation
Minimum Norm Estimate	"mne"
Weighted Minimum Norm Estimate	"wmne"
Dynamic Statistical Parametric Mapping	"dspm"
Minimum Current Estimate	"l1", "fista", "mce"
Minimum L1 Norm GPT	"gpt", "l1 gpt"
Minimum L1L2 Norm	"l1l2"

LORETA

Full Solver Name	Abbreviation
LORETA	"lor"
sLORETA	"slor"
eLORETA	"elor"

Other Minimum-norm-like Algorithms

Full Solver Name	Abbreviation
LAURA	"laura", "laur"
Backus-Gilbert	"b-g", "bg"
S-MAP	"smap"

Bayesian

Full Solver Name	Abbreviation
Champagne	"champ"
Low SNR Champagne	"lsc", "low snr champagne"
MacKay Champagne	"mcc", "mackay champagne"
Convexity Champagne	"coc", "convexity champagne"
Non-Linear Champagne	"champagne-nl"
Expectation Maximization Champagne	"emc"
Majorization Maximization Champagne	"mmc"
Full-Structure Noise	"fun"
Heteroscedastic Champagne	"hsc"
Gamma-MAP	"gmap"
Source-MAP	"source map"
Gamma-MAP-MSP	"gamma map msp"
Source-MAP-MSP	"source map msp"

Beamformers

Full Solver Name	Abbreviation
Minimum Variance Adaptive Beamformer	"mvab"
Linearly Constrained Minimum Variance	"lcmv"
Standardized Minimum Variance	"smv"
Weight-Normalized Minimum Variance	"wnmv"
Higher-Order Covariance Minimum Variance	"hocmv"
Eigenspace Scalar Minimum Variance	"esmv"
Multiple Constraint Minimum Variance	"mcmv"
Higher-Order Covariance Multiple Constraint Minimum Variance	"hocmcmv"
Reciprocal PSIICOS	"recipsiicos"
Synthetic Aperture Magnetometry	"sam"
Empirical Bayesian Beamformer	"ebb"

Artificial Neural Networks

Full Solver Name	Abbreviation
Fully-Connected Network	"fc", "esinet"
Covariance CNN	"covcnn", "covnet"
Long Short-Term Memory	"lstm"
Convolutional Neural Network	"cnn"

Matching Pursuit / Compressive Sensing

Full Solver Name	Abbreviation
Orthogonal Matching Pursuit	"omp"
Compressive Sampling Matching Pursuit	"cosamp"
Simultaneous Orthogonal Matching Pursuit	"somp"
Random Embedding Matching Pursuit	"rembo"
Subspace Pursuit	"sp"
Structured Subspace Pursuit	"ssp"
Subspace Matching Pursuit	"smp"
Structured Subspace Matching Pursuit	"ssmp"
Subspace-based Subspace Matching Pursuit	"subsmp"
Iterative Subspace-based Subspace Matching Pursuit	"isubsmp"
Bayesian Compressive Sensing	"bcs"

MUSIC/RAP/Subspace

Full Solver Name	Abbreviation
Multiple Signal Classification	"music"
Recursively Applied and Projected MUSIC	"rap-music", "rap"
Truncated Recursively Applied and Projected MUSIC	"trap-music", "trap"
Flexible RAP-MUSIC	"flex-music", "flex"
Flexible Signal Subspace Matching	"flex-ssm"
Signal Subspace Matching	"ssm"
Flexible Alternating Projections	"flex-ap"
Alternating Projections	"ap"

Basis Functions

Full Solver Name	Abbreviation
Geometrically Informed Basis Functions	"gbf"

Other

Full Solver Name	Abbreviation
EPIFOCUS	"epifocus"